Artificial intelligence empowers core facilities to stay ahead

20 March 2019
A common theme across all VIB core facilities is the generation of potentially huge datasets that require powerful analysis tools to make sense of the data being generated. As many core facilities explore state-of-the-art technologies, plenty of research is still needed to develop and benchmark data analysis tools that translate this data into new biological knowledge.

Automating data analysus with AI
Traditionally, research labs interact with core facilities to accomplish a task through direct service, consultancy or training. These are complementary types of interaction, where researchers leverage the power of artificial intelligence (AI) to empower core facilities with novel tools to better exploit the data they generate. Over the last 5 years, the Yvan Saeys Lab has pushed the boundaries of what AI techniques can do to automate data interpretation, opening up many new avenues for core facility staff as well as researchers by allowing them to gain new biological insights.

Benefiting VIB and its wider ecosystem
Together with the VIB Flow Core, the lab has been advancing the novel domain of computational flow cytometry [1]. This now facilitates high-dimensional multi-color flow cytometry analysis. The novel tools developed have been picked up by many labs, both locally within the VIB-UGent Center for Inflammation Research, and internationally. At IRC, this fruitful collaboration has led to many high-impact papers and increased industrial income for the department.

Similarly, together with the VIB Bioimaging Core (BIC), the Saeys lab has been pioneering the bio-image informatics field, empowering BIC with novel techniques for quality control, denoising, automated segmentation, and a new human-in-the-loop Fiji plugin for automated image interpretation. These tools not only shorten image processing and analysis times from weeks to days, but they also avoid biased interpretation and aim to provide robust analysis [2].

A means to ever more impactful biological insights
VIB is convinced that the interaction between research labs and core facilities regarding data analysis and novel tool development has yet to reach its full potential. As a result, it should be regarded as an avenue for further investment that will be necessary to guarantee VIB’s position at the forefront of technology development. After all, a technology is only as useful as the tools that exist to interpret the data being generated.

[1] Saeys et al., Nature Reviews Immunology 2016
[2] Roels et al., ACIVS 2016

A paper by the Yvan Saeys group was one of 2018’s ten most downloaded papers on bioRxiv. The study, ‘A comparison of single-cell trajectory inference methods: towards more accurate and robust tools’, is the first to benchmark several single-cell trajectory methods and has been accepted by Nature Biotechnology.

Go back to the overview : 'Your Research, Our Technology'


Yvan Saeys
©VIB-Ine Dehandschutter